Tutorial Molecular Docking Autodock Tools

Aplikasi yang digunakan:
1. Discovery Studio
2. Autodock Tools
3. Notepad++
4. File Kerja
Langkah-Langkah:
1. Buat file kerja dan copy paste file aplikasi autogrid4 dan autodock4
2. Download protein di RSCB dengan nama "4O75"
3. Discovery studio, file, open 4O75
4. Hapus A1, A3, Protein Group dan 2 Ligan selain RC. Chemistry, hidrogen dan add. Save dengan nama ligan.pdb. Ubah jadi Protein Data Bank Files
5. News, Open 4O75 dan hapus A2, A3 dan Ligan Group. Chemistry, hidrogen, add, add polar. Save dengan nama protein.pdb. Ubah jadi Protein Data Bank Files
6. Autodoctools, file, preferences, kolom ke 3 make default, cari tempat kerja dan set.
7. Ligan, open, file pdb nama ligan.
8. Ligan, torsion tree, detect root.
9. Ligan, torsion tree, choose root.
10. Ligan, set number torsion.
11. Ligan, torsion tree, choose root.
12. Ligan, output, save pdbqt
13. Open, protein.pdb merahkan huruf R dan hilangkah huruf L.
14. Gird, set map types, choose ligan, protein.
15. Gird, grid box, center, center on ligan, file closing saving curret.
16. Grid, output, protein.pdbqt
17. Grid, macromoleculs, open, protein.pdbqt
18. Grid, set map types, choose ligan, ligan.pdbqt
19. Grid, grid box, center ligan, hskh, output, save,ligan.gpf
20. Run, run autodocking, publi tempat file autodocking, paragnamet filname ligan.gpf
21. Docking, macromolekus, set rigid filename, protein
22. Docking, ligand, choose, ligan, accept
23. Docking, search parameter, generic algoritma, short, maximum number of evals short, accept
24. Docking, durations paramaters,, accept
25. Docking, output, lamaric GA, ligan.dpf
26. Run, run autodocking, program pathname pilih lokasi autodock4.exe, parameter filename pilih lokasi ligan dpf, launch
27. Analyze, docking, open, ligan.dlg
28. Analyze, macromolekus, open
29. Analyze, comformations, play,(protein R, ligan L)
30. Analyze, comformations, play, open panel to change play options, build current, ligan pilih S
31. File, save, write PDB, Ok,
32. Open discovery, open, ligan, ligan_conf_19, save ligan